If we use stored procedures to insert objects into the DB, how do we return the columns that the DB has automatically inserted? For example, the PK, modification timestamps and other computed fields. Can I return these as out parameters of the stored procedure?

Also, not clear to me from the hib3 documentation, can the queries using stored procedures take parameters?

For various reasons we're going to lean heavily on stored procedures for our project. Is hibernate support OK, or would we be better off with iBatis?

Since you are focused on SQL I would suggest to go with iBatis. But you can use H and iBatis simultaneously if you want:
http://sandbox.sourcelabs.com/kosta/hb- ... batis.html